John van Drie’s talk on CDK in Virtual Drug Discovery
John has started his talk this morning by giving a manifesto for open source in drug discovery. He gives an introduction to the history of virtual drug discovery, starting in 1985 (showing some dinosaur computers :-)) and then quickly jumps to y2k. While the hardware has dramatically fallen in price, the drug discovery software still costs a hundred thousand bucks. In 2015, John envisions drug discovery to be largely outsourced and distributed in a FIPnet, a network of alliances. He also believes that the limited access licensed comp chem software will be displaced by ubiquitous open source software. He encourage us to think about what single pieces of software are actually missing to get this distributed scenario.
In a second part, he jumps to explaning a typical use case, a pharmacophore-based virtual screening setup. After a historical view back, he showed his work with Rajarhi Guha on CDKPsearch. John and Rajarshi have created an XML pharmacophore description, which allows to define a pharmacophore, walk through an SDF and find fitting compounds. John has used the package in three different application scenarios with three different companies.
To finish, John brings up the question what we would need to use a pharmacophore setup to mine the data in ChEMBL, the new Chemgenomics Resource at EBI.